data_6K7J # _model_server_result.job_id iYVRmBcaTSXdFYIz3lXPgw _model_server_result.datetime_utc '2024-11-04 22:38:23' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6k7j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1201}' # _entry.id 6K7J # _exptl.entry_id 6K7J _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6K7J _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6K7J _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 B 1 NAG C 401 NAG 3 n C NAG 2 B 2 NAG C 402 NAG 3 n C MAN 3 B 3 MAN C 403 MAN # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 B SG CYS 91 C CYS 91 1_555 B SG CYS 104 C CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 B SG CYS 94 C CYS 94 1_555 B SG CYS 102 C CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 B SG CYS 157 C CYS 157 1_555 B SG CYS 171 C CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? covale ? covale1 B ND2 ASN 107 C ASN 107 1_555 G C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 B ND2 ASN 180 C ASN 180 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale3 B ND2 ASN 294 C ASN 294 1_555 F C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 C O4 NAG . B NAG 2 1_555 C C1 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? metalc ? metalc1 A OD2 ASP 414 A ASP 409 1_555 E MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc2 A O THR 416 A THR 411 1_555 E MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 6K7J _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 ACP A 1 1201 1201 ACP ACP . E 5 MG A 1 1202 1 MG MG . F 6 NAG C 1 401 404 NAG NAG . G 6 NAG C 1 402 405 NAG NAG . H 7 Y01 C 1 403 701 Y01 Y01 . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PG ACP . . . D 4 115.047 122.058 158.82 1 158.82 ? PG ACP 1201 A 1 HETATM 2 O O1G ACP . . . D 4 114.99 121.314 157.546 1 158.82 ? O1G ACP 1201 A 1 HETATM 3 O O2G ACP . . . D 4 113.735 122.97 159.005 1 158.82 ? O2G ACP 1201 A 1 HETATM 4 O O3G ACP . . . D 4 116.36 122.981 158.803 1 158.82 ? O3G ACP 1201 A 1 HETATM 5 P PB ACP . . . D 4 115.793 121.756 161.665 1 158.82 ? PB ACP 1201 A 1 HETATM 6 O O1B ACP . . . D 4 116.654 120.842 162.432 1 158.82 ? O1B ACP 1201 A 1 HETATM 7 O O2B ACP . . . D 4 114.552 122.161 162.603 1 158.82 ? O2B ACP 1201 A 1 HETATM 8 C C3B ACP . . . D 4 115.19 120.899 160.199 1 158.82 ? C3B ACP 1201 A 1 HETATM 9 P PA ACP . . . D 4 118.101 123.335 161.543 1 158.82 ? PA ACP 1201 A 1 HETATM 10 O O1A ACP . . . D 4 118.466 124.719 161.085 1 158.82 ? O1A ACP 1201 A 1 HETATM 11 O O2A ACP . . . D 4 118.871 122.15 161.034 1 158.82 ? O2A ACP 1201 A 1 HETATM 12 O O3A ACP . . . D 4 116.568 123.075 161.175 1 158.82 ? O3A ACP 1201 A 1 HETATM 13 O O5' ACP . . . D 4 118.04 123.283 163.152 1 158.82 ? O5' ACP 1201 A 1 HETATM 14 C C5' ACP . . . D 4 119.02 122.577 163.909 1 158.82 ? C5' ACP 1201 A 1 HETATM 15 C C4' ACP . . . D 4 118.582 122.462 165.362 1 158.82 ? C4' ACP 1201 A 1 HETATM 16 O O4' ACP . . . D 4 118.494 123.771 165.911 1 158.82 ? O4' ACP 1201 A 1 HETATM 17 C C3' ACP . . . D 4 117.214 121.822 165.549 1 158.82 ? C3' ACP 1201 A 1 HETATM 18 O O3' ACP . . . D 4 117.285 120.477 166.015 1 158.82 ? O3' ACP 1201 A 1 HETATM 19 C C2' ACP . . . D 4 116.528 122.636 166.622 1 158.82 ? C2' ACP 1201 A 1 HETATM 20 O O2' ACP . . . D 4 116.517 121.909 167.851 1 158.82 ? O2' ACP 1201 A 1 HETATM 21 C C1' ACP . . . D 4 117.367 123.882 166.777 1 158.82 ? C1' ACP 1201 A 1 HETATM 22 N N9 ACP . . . D 4 116.528 125.013 166.339 1 158.82 ? N9 ACP 1201 A 1 HETATM 23 C C8 ACP . . . D 4 115.826 125.066 165.195 1 158.82 ? C8 ACP 1201 A 1 HETATM 24 N N7 ACP . . . D 4 115.153 126.232 165.093 1 158.82 ? N7 ACP 1201 A 1 HETATM 25 C C5 ACP . . . D 4 115.428 126.943 166.199 1 158.82 ? C5 ACP 1201 A 1 HETATM 26 C C6 ACP . . . D 4 115.049 128.263 166.73 1 158.82 ? C6 ACP 1201 A 1 HETATM 27 N N6 ACP . . . D 4 114.219 129.078 166.041 1 158.82 ? N6 ACP 1201 A 1 HETATM 28 N N1 ACP . . . D 4 115.554 128.618 167.925 1 158.82 ? N1 ACP 1201 A 1 HETATM 29 C C2 ACP . . . D 4 116.379 127.821 168.621 1 158.82 ? C2 ACP 1201 A 1 HETATM 30 N N3 ACP . . . D 4 116.766 126.612 168.2 1 158.82 ? N3 ACP 1201 A 1 HETATM 31 C C4 ACP . . . D 4 116.328 126.131 167.021 1 158.82 ? C4 ACP 1201 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #